Newcastle disease (ND) is a deadly avian disease worldwide. In Africa, ND is enzootic and causes large economic losses, but little is known about the Newcastle disease virus (NDV) strains circulating in African countries. In this study, 27 NDV isolates from apparently healthy chickens in live bird markets of West African countries Benin and Togo during 2009 were characterized. All isolates had polybasic F protein cleavage sites and were shown to be highly virulent in standard pathogenicity assays. Infection of two-week-old chickens with two of the isolates resulted in 100% mortality within four days. Phylogenetic analysis of the 27 isolates based on a partial F gene sequence identified three clusters: one containing all the isolates from Togo and one from Benin (cluster 2), one containing most isolates from Benin (cluster 3), and an outlier isolate from Benin (cluster 1). All the three clusters are related to genotype VII strains of NDV. In addition, the cluster of viruses from Togo contained a recently-identified 6-nucleotide insert between the HN and L genes in a complete genome of NDV isolate from this geographical region. Multiple strains that include this novel element suggest local emergence of a new genome-length class. These results reveal genetic diversity within and among local NDV populations in Africa. Sequence analysis showed that the F and HN proteins of six West African isolates share 83.2 to 86.6% and 86.5 to 87.9% identity with vaccine strain LaSota, indicative of considerable diversity. A vaccine efficacy study showed that the LaSota vaccine protected birds from morbidity and mortality but did not prevent shedding of West African challenge viruses.